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Failed with int16 data

Open pieper opened this issue 1 year ago • 6 comments

I downloaded data from the TCIA / IDC C4KC-KiTS dataset and loaded a CT series. I got the error below. The int16 data type is very common for real world data so it would be great if this module worked with it.

Creating SAM predictor ... Done

Slicing along x direction
Traceback (most recent call last):
  File "/home/exouser/Downloads/Slicer-5.3.0-2023-07-08-linux-amd64/slicer.org/Extensions-31860/TomoSAM/lib/Slicer-5.3/qt-scripted-modules/tomosam.py", line 504, in onPushEmbeddingsCreate
    self.ui.PathLineEdit_emb.currentPath = self.logic.create_embeddings(output_filepath)
  File "/home/exouser/Downloads/Slicer-5.3.0-2023-07-08-linux-amd64/slicer.org/Extensions-31860/TomoSAM/lib/Slicer-5.3/qt-scripted-modules/tomosamLib/tomosamLogic.py", line 119, in create_embeddings
    self.predictor.set_image(np.repeat(img_slice[:, :, np.newaxis], 3, axis=2))
  File "/home/exouser/Downloads/Slicer-5.3.0-2023-07-08-linux-amd64/lib/Python/lib/python3.9/site-packages/segment_anything/predictor.py", line 56, in set_image
    input_image = self.transform.apply_image(image)
  File "/home/exouser/Downloads/Slicer-5.3.0-2023-07-08-linux-amd64/lib/Python/lib/python3.9/site-packages/segment_anything/utils/transforms.py", line 31, in apply_image
    return np.array(resize(to_pil_image(image), target_size))
  File "/home/exouser/Downloads/Slicer-5.3.0-2023-07-08-linux-amd64/lib/Python/lib/python3.9/site-packages/torchvision/transforms/functional.py", line 335, in to_pil_image
    raise TypeError(f"Input type {npimg.dtype} is not supported")
TypeError: Input type int16 is not supported

pieper avatar Jul 10 '23 15:07 pieper